Epilepsy is one of the most common neurological disorders, affecting as many as 1 in 26 individuals. The childhood epileptic encephalopathies (CEE) are the most severe types of epilepsy, characterized by refractory seizures, cognitive arrest or regression associated with ongoing epileptic activity, and a poor prognosis. Identifying the genetic causes of CEE is the initial step toward developing more effective diagnostic tests, prognosis counseling and treatments. Despite significant advances in gene discovery in recent years, the majority of patient with CEE remain undiagnosed. Our recent work (R01NS069605) to investigate the genetic basis of epilepsy helped establish the role of copy number variants (CNVs) in CEE. More recently, we use a high-throughput targeted sequencing strategy to screen 73 known and candidate CEE genes for mutations in a cohort of >500 CEE probands, identifying pathogenic mutations in >10% of patients. Our studies identified CHD2 and SYNGAP1 as novel and important causes of CEE, GRIN2A as a cause of epilepsy-aphasia syndromes and GABRA1 and STXBP1 as causes of a subset of SCN1A- negative Dravet syndrome. In this proposal, we build upon these successes and propose three lines of investigation. First, we will use trio exome sequencing in 150 patients with CEE who have already been screened for mutations in a large number of CEE genes and are therefore enriched for gene discovery. Second, we will use high-throughput targeted of a panel of CEE and ID genes to investigate the role of these genes in several related neurodevelopmental disorders including intellectual disability, autism spectrum disorder and schizophrenia. Finally, we will investigate the role of the chromatin remodeling pathway in epileptogenesis, highlighted by the discovery of CHD2 mutations in a subset of CEE patients. Successful completion of our aims will lead to improved genetic diagnosis of patients, better prognosis and recurrence risk counseling for families, and novel targets for development of therapeutics.